embatty

embatty's Stars

• sib-swiss/training-collection

  Collection of bioinformatics training materials

  Language:Python9644468183

• bactopia/bactopia

  A flexible pipeline for complete analysis of bacterial genomes

  Language:Nextflow3971449169

• gosling-lang/gosling.js

  Grammar of Scalable Linked Interactive Nucleotide Graphics

  Language:TypeScript159752127

• aineniamh/snipit

  snipit: summarise snps relative to your reference sequence

  Language:Python14142728

• bdusell/singularity-tutorial

  Tutorial for using Singularity containers

  1136412

• BDI-pathogens/OpenABM-Covid19

  OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic

  Language:Python111196576

• sirselim/jetson_nanopore_sequencing

  A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.

  10792512

• MultiQC/MegaQC

  Web application to collect and visualise data across multiple MultiQC runs.

  Language:Python94715928

• connor-lab/ncov2019-artic-nf

  A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

  Language:Nextflow89145389

• ukhsa-collaboration/variant_definitions

  74551819

• Wytamma/GISAIDR

  Programmatically interact with the GISAID database.

  Language:R696499

• houseofcommonslibrary/uk-hex-cartograms-noncontiguous

  Geographical templates for non-contiguous cartograms of the UK.

  677411

• CDCgov/datasets-sars-cov-2

  Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

  Language:Perl5481318

• vinuesa/get_phylomarkers

  A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

  Language:Perl514168

• W-L/ProblematicSites_SARS-CoV2

  Language:Python48121415

• agmcfarland/r_phylogenetics_worshop

  Using ggtree to build phylogenetic trees

  Language:HTML454210

• Kalan-Lab/zol

  zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

  Language:Python45254

• ncbi/sra-human-scrubber

  An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

  Language:Shell4525235

• maximilianh/multiSub

  Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

  Language:Python35432

• Psy-Fer/interARTIC

  InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

  Language:CSS295637

• LaborBerlin/score-assemblies

  Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

  Language:Python24281

• m-crown/SPEAR

  Systematic ProtEin AnnotatoR

  Language:Python192140

• ktmeaton/ncov-recombinant

  Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

  Language:Python1852272

• FredHutch/octapus

  Bacterial Operon Finder for Functional Organization

  Language:Nextflow12441

• phac-nml/rebar

  REcombination BARcode detector.

  Language:Rust126311

• covince/covince

  Tool for visualising viral lineages in space and time. As seen on covid19.sanger.ac.uk and covglobe.org.

  Language:JavaScript104264

• MDU-PHL/pango-collapse

  app to collapse Pango lineages for reporting

  Language:Python103121

• phac-nml/ncov-dehoster

  Removal of human reads from ncov nanopore sequencing data

  Language:Nextflow57124

• fmaguire/vector_figures

  Collection of conceptual SVG figures created by me for talks

  420

• learithe/epifish

  Package for creating epi-curve fishplots

  Language:R3311